Transcriptomic and spliceosomic landscapes of pancreatic neuroendocrine tumors generated through Oxford Nanopore Technology sequencing (A18)

Introduction: Pancreatic Neuroendocrine tumors (PanNETs) are rare neoplasms with heterogenous
nature, still poorly understood. Their low mutational burden has prompted to explore other molecular
aspects, from epigenomics to transcriptomics. Increasing evidence indicates that transcriptomic
changes, often derived from alterations in alternative splicing, can generate isoforms with oncogenic
potential. In this context, long-read Oxford Nanopore Technology (ONT) has emerged as an ideal suited
sequencing tool to deeply study transcriptomics and splicing variants.

Aim(s): To achieve a detailed characterization of PanNETs transcriptomic and spliceosomic landscapes using new sequencing tools to gain further understanding of their molecular architecture and identify new biomarkers and actionable targets.

Materials and methods: We used ONT to sequence cDNA from a set of 8 PanNETs and 3 reference tissues. After a quality check (pycoQC), we used the software EPI2ME to preprocess, identify
full-length reads, trimming and correct the orientation. Then, we mapped the sequences to the human
reference genome (minimap2); assembled the sequences (stringtie); compared to the reference
annotation (gffcompare) and detected fusion genes (JAFFAL).

Results: Study of high RNA quality samples enabled us to identify numerous annotated and novel transcripts, highlighting 10 novel transcript variants present in PanNETs but not in non-tumor tissues, and fusion genes (outstanding 166 fusion genes with GNAS), which may be relevant in NETs. Conclusion: These initial results indicate that long-read sequencing with ONT leverages the precision and depth of transcriptomic knowledge extracted from NETs, which can help to better understand their molecular architecture and, ultimately, explain their clinical behaviour.

Keywords: pancreatic neuroendocrine tumor, oxford nanopore technology sequencing, transcriptomics, splicing, fusion genes